Target Decoy approach

1 Pyrococcus

source('https://statomics.github.io/SGA2020/assets/EvalTargetDecoys.R')
library(mzID)
mzIdMsgfPlus<-mzID("~/Dropbox/statOmics/SGA2020/identification/pyrococcusMSGF+.mzid")

## reading pyrococcusMSGF+.mzid... DONE!

1.1 PPplots

decoyPlots <- evalTargetDecoys(mzIdMsgfPlus,decoy="isdecoy",score="ms-gf:specevalue",log10=TRUE)

## Warning: Removed 9387 rows containing missing values (geom_point).

decoyPlots

## $ppPlot

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## $histogram

## 
## $ppPlotZoom

## Warning: Removed 9387 rows containing missing values (geom_point).

## 
## $histogramZoom

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## $together

2 Information on the package version

sessionInfo()

## R version 3.6.0 (2019-04-26)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS  10.15.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C/UTF-8/C/C/C/C
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] shiny_1.3.2   ggpubr_0.2.5  magrittr_1.5  ggplot2_3.3.0 dplyr_0.8.2  
## [6] mzR_2.18.0    Rcpp_1.0.1    mzID_1.22.0  
## 
## loaded via a namespace (and not attached):
##  [1] later_0.8.0         pillar_1.4.2        compiler_3.6.0     
##  [4] plyr_1.8.4          base64enc_0.1-3     tools_3.6.0        
##  [7] iterators_1.0.10    ProtGenerics_1.20.0 ncdf4_1.16.1       
## [10] digest_0.6.19       evaluate_0.14       jsonlite_1.6       
## [13] tibble_2.1.3        gtable_0.3.0        pkgconfig_2.0.2    
## [16] rlang_0.4.6         foreach_1.4.4       yaml_2.2.0         
## [19] parallel_3.6.0      xfun_0.8            stringr_1.4.0      
## [22] knitr_1.23          withr_2.1.2         cowplot_1.0.0      
## [25] grid_3.6.0          tidyselect_0.2.5    glue_1.3.1         
## [28] Biobase_2.44.0      R6_2.4.0            XML_3.98-1.20      
## [31] rmarkdown_2.3       purrr_0.3.3         promises_1.0.1     
## [34] scales_1.0.0        codetools_0.2-16    htmltools_0.3.6    
## [37] BiocGenerics_0.30.0 assertthat_0.2.1    xtable_1.8-4       
## [40] mime_0.7            colorspace_1.4-1    httpuv_1.5.1       
## [43] ggsignif_0.6.0      labeling_0.3        stringi_1.4.3      
## [46] doParallel_1.0.14   munsell_0.5.0       crayon_1.3.4